Navigation Menu is somehow hidden when I use a menu plugin

I am trying to build a nice looking Nav menu, and I'm getting so frustrated with the lineup of issues.

I have tried both UberMenu and WR Mega Menu plugins and different problems occur with both. I have created a new thread because the problem has now changed.

Originally I believed this to be a javascript error caused by visual composer. I tested both plugins with visual composer (and accompaning plugins) deactivated, and here were the results.

UberMenu: Loading message on Appearance > Menus would not dissappear (said it was a common js error). Once VC was deactivated this message went away, and UberMenu seemed to load fine.

WR Mega Menu: The js mega menu builder would not appear until VC was deactivated.

Now that VC is deactivated, the menu should have appeared just fine, but it didn't. I used firebug (equivalent) to see that the Nav visibility was set hidden. I tried changing it to visible but this was overwritten each time.

I cannot figure out why the Nav is hidden when either plugin is used. In order to test this, you must deactivate; Visual Composer, PW Post Grid, and VC Ultimate Addons !AT THE SAME TIME otherwise sitewide failure requiring FTP access to fix

Access has been granted to my site to replicate the issue please deactivate all three plugins at the same time, and activate either WR Mega Menu or UberMenu and you will see my Nav disappears altogether.

All my custom css is located in Appearance>Suffusion Options>Backend>Custom Includes